Note of some special PDB Entry

Content

5VGA

PubMed: 29113027

Re-refinement Note

This entry reflects an alternative modeling of the original data in:

• 2A6I - determined by Sethi, D.K., Agarwal, A., Manivel, V., Rao, K.V., Salunke, D.M.

4CSC

With UNK residue

Identity Value Error

• 6BCU (with Q8N122 and Q8N122-2)
• 3VKL (with O00214)
  • possiblely caused by invalid alignment
• 3b3q_A (with Q99K10, 0.93)
  • error alignment range

Feedback to EMBL-EBI

Hi, I am implementing the REST calls based on SIFTS mappings to get Range-mapping between PDB-chain and UniProt-Isoform. However, I found some error-prone information in the results. Here is an example:

GET: https://www.ebi.ac.uk/pdbe/api/mappings/all_isoforms/6bcu

And I Got Q8N122's [2,1335] mapped with 6bcu W chain's [10,1343] with identity 0.19. But the alignment of these two sequences shows that they are identical in the mapped range and there are only 9 residues of 6bcu_W and 1 residue of Q8N122 outside the range.

I am confused about the result. Could you please help me figure out this issue?

(2020-02-29)

1ABN

• CA ATOMS ONLY

6B6U

• with mutation

6OAK

• with modified res

ho but he

• 6HQU
• 1b35

3O77

• in multi organism
• 17 muta

4u6f,4v8z,6n8m,6fs0,1o0e

• with UNK residue

Contains Hybrid DNA/RNA

• 6ozg

Best mapped to non canonical seq

• 5ewl (best mapped to A0A1L8F5J9-8)
• 1b8i (entity 3 best mapped to P83949-5)

Has multi tax

• 5edu
• 6rz6
• 6bqh

Muti tax he

• 6W1D

Wrong Message

• 6ox4
  • 39个配体分子, 但是pdbe-graph-api(graph db)给出26个, 少了

Similar Sequence

• 3lpa (with uniprot: A5EXI3, tax: Dichelobacter nodosus VCS1703A)
• 3lpc (without uniprot, tax: Dichelobacter nodosus)

More:

Alignment Problem

• 4c66 (可以从1开始map,但是sifts从3开始, with O60885)

Multiple method_class

• 1iob (INTERLEUKIN-1 BETA FROM JOINT X-RAY AND NMR REFINEMENT)

MMCIF 与 PDB 文件中标号存在差异

• 4fbq

PDB中的各种链

Reference

常见类型

• polypeptide(L)
• polyribonucleotide
• polydeoxyribonucleotide

特殊类型

• polydeoxyribonucleotide/polyribonucleotide hybrid
• polypeptide(D) (e.g.3ue7, struct_asym_id: A)
• cyclic-pseudo-peptide (e.g.3q9h,6iqg BUT polypeptide(L) was asigned to entity_poly.type)
• other

新兴类型

• carbohydrate polymer (e.g.6iqg)

目前已知PDBe API会返回的类型

• polypeptide(L)
  • NOTE: 含有部分非常见的链, 如上述提及的cyclic-pseudo-peptide
• polyribonucleotide
• polydeoxyribonucleotide
• bound
• water
• polypeptide(D)
• polydeoxyribonucleotide/polyribonucleotide hybrid

1WDQ

• 没了MAL配体
• 多了碳水化合物GLC

PDB with Insertion Code

• 3sqh

Asymmetric unit of 3sqh

# 
loop_
_pdbx_poly_seq_scheme.asym_id 
_pdbx_poly_seq_scheme.entity_id 
_pdbx_poly_seq_scheme.seq_id 
_pdbx_poly_seq_scheme.mon_id 
_pdbx_poly_seq_scheme.ndb_seq_num 
_pdbx_poly_seq_scheme.pdb_seq_num 
_pdbx_poly_seq_scheme.auth_seq_num 
_pdbx_poly_seq_scheme.pdb_mon_id 
_pdbx_poly_seq_scheme.auth_mon_id 
_pdbx_poly_seq_scheme.pdb_strand_id 
_pdbx_poly_seq_scheme.pdb_ins_code 
_pdbx_poly_seq_scheme.hetero 
...
A 1 179 TRP 179 148 148 TRP TRP E . n 
A 1 180 THR 180 149 149 THR THR E . n 
A 1 181 ALA 181 149 149 ALA ALA E A n 
A 1 182 ASN 182 149 ?   ?   ?   E B n 
A 1 183 VAL 183 149 ?   ?   ?   E C n 
A 1 184 GLY 184 149 ?   ?   ?   E D n 
A 1 185 LYS 185 149 ?   ?   ?   E E n 
A 1 186 GLY 186 149 ?   ?   ?   E F n 
A 1 187 GLN 187 149 ?   ?   ?   E G n 
A 1 188 PRO 188 152 152 PRO PRO E . n 
A 1 189 SER 189 153 153 SER SER E . n 
...

1C7C

DEOXY RHB1.1 (RECOMBINANT HEMOGLOBIN)

Genetically crosslinked hemoglobin: a structural study.

Asymmetric unit of 1c7c	Asymmetric unit of 1c7b

Seems to have multiple model but not split into multiple model

• 1gjj
• 6hx3

Asymmetric unit of 1gjj	Asymmetric unit of 6hx3

Insertion

• 6qh5
• 2x2e
  • linker
• 3zyc

2x2e_A, selected insertion region (aligned with Q05193)

Deletion

• 5kwa
• 3b3q

Insertion Plus Deletion

• 6hei: Entity 1 (InDel_1)
• 5d3q (InDel_1)
• Q07817-2
  • 6vwc_B InDel_1
  • 2o2m_A InDel_2
  • 2p1l_A InDel_3
• O15519-8
  • 3h11_A InDel_3

6hei_A, selected insertion region (aligned with Q96RU2-3)

C/N-Terminal Addition

• P0AEX9
  • 6ki0
  • 4wrn
  • 5t05
  • 4gx8
  • 4d4o (special)
    • A
    • B
    • C
  • …

Hybrid

• 6qgj
  • P10415
  • Q07817

Bound to many ligands

• 2cvc
• 6clz
• 6cm1

Asymmetric unit of 2cvc	Asymmetric unit of 6clz