Structure of PDB 6ydw Chain BC

Receptor sequence

>6ydwBC (length=694) Species: 9606 (Homo sapiens)

VIPNEKIRNIGISAHIDSGKTTLTERVLYYTGRIAKMHEVKGKDGVGAVM
DSMELERQRGITIQSAATYTMWKDVNINIIDTPGHVDFTIEVERALRVLD
GAVLVLCAVGGVQCQTMTVNRQMKRYNVPFLTFINKLDRMGSNPARALQQ
MRSKLNHNAAFMQIPMGLEGNFKGIVDLIEERAIYFDGDFGQIVRYGEIP
AELRAAATDHRQELIECVANSDEQLGEMFLEEKIPSISDLKLAIRRATLK
RSFTPVFLGSALKNKGVQPLLDAVLEYLPNPSEVQNYAILNKKTKILMNS
SRDNSHPFVGLAFKLEVGQLTYVRSYQGELKKGDTIYNTRTRKKVRLQRL
ARMHADMMEDVEEVYAGDICALFGIDCASGDTFTDKANSGLSMESIHVPD
PVISIAMKPSNKNDLEKFSKGIGRFTREDPTFKVYFDTENKETVISGMGE
LHLEIYAQRLEREYGCPCITGKPKVAFRETITAPVPFDFTHKKQSGGAGQ
YGKVIGVLEPLDPEDYTKLEFSDETFGSNIPKQFVPAVEKGFLDACEKGP
LSGHKLSGLRFVLQDGAHHMVDSNEISFIRAGEGALKQALANATLCILEP
IMAVEVVAPNEFQGQVIAGINRRHGVITGQDGVEDYFTLYADVPLNDMFG
YSTELRSCTEGKGEYTMEYSRYQPCLPSTQEDVINKYLEATGQL

3D structure

• PDB: 6ydw Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1.
• Chain: BC
• Resolution: 4.2 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	BC	Q396 S543 Q548 K580 I624	Q348 S495 Q500 K532 I576
BS02	rna	BC	Q542 S543 G544	Q494 S495 G496
BS03	rna	BC	I55 D56 R98 R178 K541 R628 K635 Q661 I665 A666 N669 R670 I675 T676 G677 T701 R704 S705 E708	I16 D17 R59 R139 K493 R580 K587 Q613 I617 A618 N621 R622 I627 T628 G629 T653 R656 S657 E660
BS04	GNP	BC	D56 S57 G58 K59 T60 T61 V79 T101 N174 K175 D177 S299 L301	D17 S18 G19 K20 T21 T22 V40 T62 N135 K136 D138 S260 L262
BS05	MG	BC	T60 T101	T21 T62

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding

Biological Process

• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0070125 mitochondrial translational elongation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix

External links

• PDB: RCSB:6ydw, PDBe:6ydw, PDBj:6ydw
• PDBsum: 6ydw
• PubMed: 32602580
• UniProt: Q96RP9|EFGM_HUMAN Elongation factor G, mitochondrial (Gene Name=GFM1)